Summary:

The authors measured negative atmospheric ions above the SMEAR II boreal forest site from a novel aircraft platform. Level flight legs were performed in the stable boundary layer, residual layer, mixed layer, and free troposphere at various times of day across several weeks. The measurements illustrate the evolution of negative ions in the atmosphere as the boundary layer rises. Ion composition is variable between different layers on each day, and variable within each layer across different days due to changes in airmass history. I found this paper to be very clearly written and depicted, and it is a useful contribution to the knowledge of atmospheric ions and their impacts on new particle formation. I have just a few minor comments below, and recommend publication in ACP.

Comments:

Line 176: Can you provide more details here for readers who may be unfamiliar with sampling with an APi-TOF, e.g., are ion transmission rates of ~1% normal? How do your transmissions rates compare with previous field measurements of ions, or with the ground measurements at the SMEAR II site?

Line 220: When the flight setup was operated in the tower, did it include the same sliding inlet system to see if the inlet contributed to any differences between instruments?

Line 374: You are saying the FT air had marine origin in both morning and afternoon flights on 2 May 2017. You justify this as the reason for measuring halogenated compounds in the morning and MSA in the afternoon. Do you have any thoughts on why the halogenated compounds were not present in the afternoon and MSA was not present in the morning? Is this a result of charge transfer, as you discuss later on (e.g. line 438), or something else?

Line 478: I wonder if you find any correlation between ground level monoterpene concentrations and/or ozone concentrations with HOM in the SBL. Maybe there is a way to explain some of the slight variations in HOM across different days. Were there monoterpene measurements at SMEAR II during these times?

Fig S2: Can you color by altitude? That would help make the plot clearer I think.

General comment: This paper focuses mainly on presenting the data, and it would be even more useful if you could expand upon what these results mean for atmospheric processes that depend on ions. For instance, what does the variable distribution of negative ions mean for the likelihood of NPF in each different layer of the atmosphere? Is NPF favored by the ions found in the boundary layer and mixed layer, or disfavored by the lack of HOM in the free troposphere? Please expand somewhere, perhaps in the conclusions section, even if it is to clarify that not enough is known yet about what role each subclass of ions ultimately plays in NPF.

Summary and general comment:

This study by Beck et al. characterizes the atmospheric negative ion composition of various tropospheric layers (from 100m to 3200m) above the SMEAR II research station in the Finnish boreal forest. By deploying an API-TOF mass spectrometer in a Cessna 172 aircraft, the authors resolved the vertical distribution and diurnal variation of naturally charged molecular ions and ion-clusters from the stable boundary layer up to the free troposphere. While the ion composition of the stable boundary layer coincides with the simultaneous measurements placed at the field station on top of a 35m tower above the forest canopy, the other layers showed a clearly distinguishable ion composition. In the residual and mixing layers, the ion composition is strongly dependent on the origin of air masses, the turbulent mixing, and the photochemistry throughout the day. Most of the detected ions during daytime are comprised of sulfur-containing compounds, while the nocturnal ion compositions are more diverse. The detection of various halogens and carboxylic acids as well as the absence of HOMs in the free troposphere indicates that this layer is mainly influenced by long-term transported air mass.  

I agree with the general comment by reviewer 1. The authors realized a difficult technical measurement and showed through comprehensive investigations the composition and chemical processes of negative ions in various tropospheric layers and their diurnal evolution. The methods are extensively illustrated and clearly written, enabling a good evaluation of the results by the scientific community, and promoting a continuation of the study in this field of research. However, the manuscript lacks a detailed discussion and developed conclusion of the atmospheric implication to obtain a comprehensive understanding of ion chemistry and its role for NPF in the various tropospheric layers. I would recommend the manuscript for publication in ACP as a measurement report after the following minor comments have been addressed. 

Minor comments:

Line 35ff.: Please also consider the earlier work of Yu, F., and R. P. Turco (2001), From molecular clusters to nanoparticles: Role of ambient ionization in tropospheric aerosol formation, J. Geophys. Res., 106, 4797–4814, 10.1029/2000JD900539. 

Line 49: Please also consider the earlier work of Lovejoy, E. R., Curtius, J., Froyd, K. D. (2004), ‘Atmospheric ion-induced nucleation of sulphuric acid and water’, J. Geophys. Res. 109, 10.1029/2003JD004460.

Line 153: I wonder if the active ionization by the x-ray source during the flights might provide some helpful information (even of its short period) to support some conclusions.

Line 155: Did you observe a significant variation of the total ion count (TIC or ions per second, including transmission correction) during the flights in the different tropospheric layers or times of the day? 

Line 163ff.: You may add the TIC to Figure S2 if there is a variation.

Line 164ff.: Can you estimate qualitatively how strong the measurements can be influenced by the pressure changes (e.g., transmission and ion-cluster stability).

Figure 5: Please mention the black dotted line and its meaning in the figure caption.

Line 371ff: Similar to reviewer 1; you showed that during daytime MSA is present in the FT, while iodic acid and halogenated compounds are almost absent. On the basis that the measured air mass had a marine origin (as shown in Fig. S15), can you elaborate a bit more on your conclusion? Typically, you would expect all species from marine sources. Can MSA also be formed by a different source, e.g., degassing of MSA from dehydrated aerosol (Zhang et al. (2014); doi: 10.1002/2014GL060934).

Figure 7: What element composition corresponds to the strong iodine peak in between the sulfur-containing molecules close to 200Th? Please mark/add this one also in table A1.

Line 409ff.: Are any ammonia-containing clusters measured at the ground station during this time to support your conclusion for this case study?

Line 436ff.: The concentration of HOM dimers and iodic acid could also be reduced due to NPF or atmospheric chemical processes. In my opinion, the statement “their charges being transferred to SA” is not fully valid here. Please elaborate a bit more on this conclusion.

Figure 6 + 10: You may want to add the estimated sulfuric acid concentration also in these figures as shown in Figure 7b.

Figure 11+12+13+14+16+18: Why are the detected HOMs (shown in the figures before and table A1) now combined with all (unidentified ion compounds)?

Technical comments:

Line 254: better use "sources of uncertainty" instead of "source of error".

Line 276: better use "upward trend" instead of "buoyancy". 

Line 385: The estimated sulfuric acid concentration […] varied from 0.3 to 1·10⁶ cm^-3 and […]. 

Line 402: reference should be Fig. S15, not S6.

Line 505: You may focus the reader on the trajectory you referring to (e.g., Fig. S14 blue trace).

Reference to Fig. S17 is missing.